The answer's already been hashed and re-hashed in here, but for old times' sake I'll give it another whirl.

1. Character Development: An initially weak-willed protagonist can offer a multitude of story possibilities which can work to develop him. Simon from Gurren Lagann is a great example as he begins the series a young boy who relies totally upon his older friend ("bro") Kamina, to help him figure out what he should fight for and to bring up the will to fight for it. But, throughout the series, he grows due to "situations" which lead him to ultimately become a Kamina-like figure for all of Team Dai-Gurren (and humanity, as well), as he becomes more independent and strong-willed.

2. Symbolism: A character who often seems weak-willed is actually supposed to represent some other idea. Shinji Ikari, for example, represents the part of the human psyche which differentiates between right and wrong, just as Rei Ayanami represents the logic portion, and Asuka Langley Soryu represents the emotional/impulsive portion. (Read about Freud's Id, Ego, and Super-Ego if you need to know more). So when Shinji enters a situation which is morally ambiguous, or which he does not know enough to morally justify either action, he winds up incapable of doing anything other than masturbating and hating himself (as implied by the "End of Evangelion" dream sequence/acid trip) because he can't psychologically support either option.

3. Realism: It isn't all too often in real life that we meet people who ACT confident AND who actually ARE confident. And, as most anime series focus on a child/teenage/young adult main character or protagonist, and as younger people are usually even more self-conscious than the majority of people in general, it would seem more realistic for these younger characters to be weak-willed or to lack confidence. And, as it's usually considered more entertaining to sympathize or understand a character, by making them more realistic, it heightens a viewer's ability to feel that sympathy/understanding. Thus, ultimately, it makes the show more likely to be entertaining.

These are the three primary reasons for weak-willed characters, though the symbolism approach isn't used nearly as often as the other two (Character Development and Realism).

I would settle for a half way competent male character, even if it was someone out of their position or in water over their head. If they would just not act completely idiotic. Occasionally competent adults that help, would be a positive change.

I think the anime industry likes the character-development phase. It's a bit hard to lengthen an anime a lot if you already have a main character who's super badass and doesn't have much room to grow.

Plus, it's not like as if Japan is filled with buff and masculine guys and all (Yes, there's some, but I'm talking about in general).
That being said, it could also be an incentive/appeal for viewers because it's inspiring.

My favorite anime of all time, Hajime No Ippo, severely embodies the frail newb -> legend idea, so I guess it also depends on how the characters go through the development process.

I personally would like an anime which you describe, but sadly I haven't seen one that's really like that yet except for Hellsing.

I'm also a bit annoyed with all these long-haired 14-16 year old kids, who are shown as if they look like they're in their mid 20's, saving the world. It would be nice to see an anime that makes sense with realistic characters for a change.

I'm not a fan of wimpy leads unless they go through notable character development to become stronger. As for the design, since I notice people talking about this, I'll comment on that too. I could care less if they have an effeminate edge to them. The bishonen look is meant to appeal to the female demographic and honestly, hyper-masculinity, short hair, and buffness is so promoted in American culture, that I've come to prefer Japan's twist on things. Funny thing is anime does still feature a variety of designs and I've seen my share of arguably masculine looking leads.

It seems like once you get out of the top shonen animes like One Piece, Fairy Tail, Gintama, Naruto, and Bleach that there is a over whelming trend towards male main characters being weak willed and whimpy usually accompanied by a strong female character. why is this? Is it really that popular in Japan to have male main characters like that?

Yeah, I'm pretty sure it has to do with relating to them or whatever. But it pisses me off if they aren't a badass by the end of the show.

Yeah I'm of the same opinion here... All those weak annoying main characters were "designed" that way so you can relate to them, which actually sucks. Another reason behind it might be to ensure an interesting character development...

But then again... Which anime main characters are strong and badass nowdays? (that era it's pretty much over, there are a few exceptions though: Gintoki-sama praised be...)

Yeah, I'm pretty sure it has to do with relating to them or whatever. But it pisses me off if they aren't a badass by the end of the show.

Yeah I'm of the same opinion here... All those weak annoying main characters were "designed" that way so you can relate to them, which actually sucks. Another reason behind it might be to ensure an interesting character development...

But then again... Which anime main characters are strong and badass nowdays? (that era it's pretty much over, there are a few exceptions though: Gintoki-sama praised be...)

Yeah, the character development is a biggie. But every now and then, the character barely even develops, and even in the end they're a big freakin' sissy. It angers me to no end. But even in the beginning when they're weak and relatable or whatever, it's just hard to watch them. They're so dang annoying.

Aging a strong male character does not necessarily impede character development. You can use his super awesomeness to build what is around him and alter his train of thought or tell the story "" which is built to support why the character is so. I wouldn't say there are less protagonists just an increase in the amount of whimpy protagonists-kun.

I will say that actually weak personalities are not all that common as many others pointed out, many characters have slight weaknesses but mainly they are solid. You do get the occasional wimp or dufus in some harem shows. Shojo manga male characters usually have very solid personalities.

I think the question becomes, why are characters outside of shonen manga usually so frail looking. Lelouch from Code Geass, Keima from TWGOK, Kirito from SAO. They all have resilient personalities, Kirito could be considered a superman archetype. They are all frail looking though. I think this mainly comes from just societal aesthetic values in Japan.

Little boys tend to want to grow up and be strong, so they like beefy characters. Once they reach middleschool though, only a portion of them remain interested in sports, the others are overwhelmed with studying, and the majority of them become frail and skinny. Japanese girls at the same time tend to fall for that girly idol type of guy, so some guys strive for that. On the other hand, even people who are adequately muscly are extremely rare in Japan. So when you have a lot of animes based in the real world, and around romance, you tend to have characters that represent one of two things, either the average Japanese male who is reserved and skinny, or the male idol who is skinny and flashy.

In the U.S. our cultural icons are the military, fire fighters, astronauts, super heroes, American Football players, and martial artists. No matter who, we admire well built (beefy), confident men. Although there is tolerance, generally the image of either the idol or the average skinny guy, is viewed as being weak and wussy, teenage boys viewed as immature. That is why generally in our movies, characters are usually older and beefier.

The plot would be too "perfect". You can't have too many perfect characters. Even though those characters are near perfect though, the author lazily wanted them to appear imperfect by giving them a shitty personality but the power to do anything they fucking want. They can be a pussy and still get laid by a hot chick.
Anime characters make no sense most of the time, though.